Tears filled Ricardo Pineda’s bloodshot eyes as he relived the solitude and paranoia of his 13-day march to safety.

Five hours earlier, after almost a fortnight on the run, he had slipped over Nicaragua’s southern border, flagged down a taxi and taken his phone off flight mode for the first time since fleeing Managua.

Now the sleep-deprived doctor was sitting in a safe house on the outskirts of Costa Rica’s capital contemplating the sudden unraveling of his country and the start of a new and uncertain life in exile.

“It’s terrifying because you know they are tracking you ... every footstep, every little noise, every branch, every tree – you think it’s the army and they’re going to grab you ... you’re a fugitive,”said Pineda, 54, who bolted after receiving death threats for treating the victims of Daniel Ortega’s crackdown on protesters and denouncing those killings.

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'We are not afraid' Why are Nicaraguans protesting? – video explainer

While people fleeing violence in El Salvador, Honduras and Guatemala have sought safety by heading north towards the US, Nicaraguans have long headed south. For more than a century Nicaraguans, among them many of Ortega’s fellow Sandinistas, have looked to Costa Rica for sanctuary from crisis, repression and war. A display at San José’s National Museum pays tribute to the nicaragüense economic migrants who came “looking for a more promising future for their families”.

But the thousands of asylum seekers now crossing the border each month say they seek survival, not service. “If I go back they’ll kill me,” said Fraol Espinosa, a 31-year-old protester from León who claimed paramilitaries had torched his house in retribution for his role erecting barricades during the anti-Ortega insurrection.

Last Thursday night Espinosa was one of dozens of Nicaraguan refugees packed into a pink and green love motel in San José’s red light district, one of perhaps a dozen such establishments now housing those fleeing the strife. Sharing room 16 with him were six other protesters from Masaya, Jinotega, Diriamba, Matagalpa and Ometepe, other rebelling towns that were recently retaken by Ortega’s forces.

Next door, in room 17, a family of five perched on the double-bed on which they would spend their first night in exile. “We had to come because we took part in the ‘blue and white’ march,” explained Amparo Rios, 38, breaking down as she recalled abandoning her three children, aged nine, 14 and 16, after being threatened and attacked by paramilitaries.

Her cousin, Gloria Isabel Mendoza, tried to comfort her: “Here at least we’re safe. We have nowhere to live. But at least there’s no shooting.”

Members of San José’s large Nicaraguan community say they began receiving asylum seekers soon after the uprising began late April. But that trickle turned into a daily tide earlier this month after rifle-toting security forces and paramilitaries launched an all-out assault on rebel strongholds dubbed “Operación Limpieza”. Activists say that onslaught pushed the death toll to almost 450.

If you were involved in any way, you are a target ... They are being hunted

Maria Elizondo, activist

“It started when Ortega decided to clean house violently,” said Maria Elizondo, the founder of a local activist group providing support, food and medical care to the displaced. “If you were involved in any way, you are a target ... They are being hunted.”

Those now on the run include journalists, human rights activists and doctors like Pineda, a former army medic who fled Managua on 14 July after surviving an 18-hour church siege that left two dead and drew international condemnation. A draconian new “anti-terror” law, which campaigners say allows authorities to criminalise the opposition by classifying almost any kind of political dissent as terrorism, has added to their sense of dread.

But the displaced also include children and teenagers, like Brandon Sandoval, who have little grasp of the turmoil engulfing their country.

“He’s 14,” said Sandoval’s grandmother, Flor del Carmen López, 69, her grief turning to rage as she explained how the boy’s father had begged her to take him south to protect him from the violence. “‘Flee - because I’m not going anywhere!” she remembered him telling her. “I’m staying put to defend Nicaragua!”

A Nicaraguan living in Costa Rica demonstrates in support of the anti-government resistance. Photograph: Juan Carlos Ulate/Reuters

Fernando Sánchez, a student protest leader who is currently lying low on the rural outskirts of Costa Rica’s capital, insisted the protests were “a peaceful insurrection” against a murderous and dictatorial regime. “We have never been on the side of violence or the guns. This side belongs to Daniel Ortega and the butchers who work with him,” said the 20-year-old.

But in the plaza outside San José’s Our Lady of Mercy church – a palm-dotted magnet for newly arrived Nicaraguans seeking contacts and shelter – more radical proposals were floated as exiles debated Ortega’s refusal to step down and tempers frayed.

“The solution is an invasion: to invade Nicaragua and free this nation!” roared Carlos Gutiérrez, 50, from Matagalpa.

“We want an intervention .... a North American intervention! The blue helmets!” shouted 39-year-old Erick Blandón.

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Miguel Martínez, from Jinotega, nodded in agreement: “[Ortega] won’t go quietly. Bullets are the only thing he understands.”

For all that indignation, the priority for most of the penniless and disorientated exiles turning up in San José remains basic survival. Many now reside in seedy flophouses or homeless shelters on the city’s skid row while others camp on street corners, crash under trees or have been taken to a government shelter further south near the border with Panama.

As darkness fell and new arrivals prepared for their first night in a foreign land, sex workers in red mini-skirts assembled outside the Molino Rojo nightclub on Avenida 10. Over the road, the Colombian pastor Kristtal Gonzales Sanabria offered a tour of her cockroach-infested temple, the Compassion of Jesus church, where almost every conceivable space, including the altar, is now occupied by dozing migrants – 90% of them Nicaraguans.

“It’s so sad ... They don’t know whether to walk east or west or north or south. They don’t even know what will happen tomorrow,” said Sanabria, herself a migrant driven from her home Saldaña inColombia after her husband was kidnapped and killed by the guerrillas of the Revolutionary Armed Forces of Colombia, Farc.

Children forced to flee Nicaragua with their parents outside the Our Lady of Mercy church. Photograph: Tom Phillips for the Guardian

At the shelter’s entrance she had posted a copy of Psalm 91. “He who dwells in the shelter of the Most High will rest in the shadow of the Almighty ... You will not fear the terror of the night, nor the arrow that flies by day,” it said.

Shortly before 11pm, the latest group of Nicaraguan émigrés arrived from Masaya, led by 23-year-old Oscar Rosales Sánchez. “Thank God I made it out,” said Sánchez, whose father had not had the same luck.

“They shot him once in the head and once down here,” he explained motioning to the left side of his abdomen.

After a few hours sleep, Sánchez headed to the park outside Our Lady of Mercy, fuming as he shared his story to a dozen outraged exiles with almost identical tales of dissent and death. “We will go back to avenge the deaths of all our brothers,” he vowed, fighting back the tears.

“That’s what I like to hear!” screamed López, the fleeing grandmother, who was also among the crowd. “This hasn’t finished! This is just getting started!”

All around them destitute Nicaraguans began to chant. “Viva Nicaragua!” they cried. “Nicaragua will be free!”